Co-phylog: an assembly-free phylogenomic approach for closely related organisms

With the advent of high-throughput sequencing technologies, the rapid generation and accumulation of large amounts of sequencing data pose an insur-mountable demand for efficient algorithms for con-structing whole-genome phylogenies. The existing phylogenomic methods all use assembled se-quences, which are often not available owing to the difficulty of assembling short-reads; this obstructs phylogenetic investigations on species without a ref-erence genome. In this report, we present co-phylog, an assembly-free phylogenomic approach that creates a ‘micro-alignment ’ at each ‘object ’ in the sequence using the ‘context ’ of the object and cal-culates pairwise distances before reconstructing the phylogenetic tree based on those distances. We explored the parameters ’ usages and the optimal working range of co-phylog, assessed co-phylog using the simulated next-generation sequencing (NGS) data and the real NGS raw data. We also compared co-phylog method with traditional align-ment and alignment-free methods and illustrated the advantages and limitations of co-phylog method. In conclusion, we demonstrated that co-phylog is efficient algorithm and that it delivers high resolution and accurate phylogenies using whole-genome unassembled sequencing data, especially in the case of closely related organisms, thereby sig-nificantly alleviating the computational burden in the genomic era